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The work was supported by the Copernicus Marine Environment Monitoring Service (CMEMS) LATEMAR project. CMEMS is implemented by Mercator Ocean in the framework of a delegation agreement with the European Union. This work has also been conducted as part of the bilateral project EOLO-1 (“Extreme Oceanic waves during tropical, tropical-like, and bomb cyclones”) between CNR-ISMAR and the University of Tokyo (Japan; Prof. Takuji Waseda). Antonio Ricchi funding have been provided via the PON “AIM” - Attraction and international mobility program AIM1858058. Joanna Staneva acknowledges H2020 IMMERSE Project, Arno Behrens was supported by CMEMS Waveflow project and G. Gayer by ESA Black Sea and Danube Regional Initiative (EO4BS). Issue sup1: Copernicus Marine Service Ocean State Report, Issue 5 Supplement.-- Karina von Schuckmann (Editor), Pierre-Yves Le Traon (Editor), Neville Smith (Chair) (Review Editor), Ananda Pascual (Review Editor), Samuel Djavidnia (Review Editor), Jean-Pierre Gattuso (Review Editor), Marilaure Grégoire (Review Editor),

Copyright © 2012 Anti Vasemagi et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. peer-reviewed Domesticated animals provide a unique opportunity to identify genomic targets of artificial selection to the captive environment. Here, we screened three independent domesticated/captive Atlantic salmon (Salmo salar) strains and their wild progenitor populations in an effort to detect potential signals of domestication selection by typing of 261 SNPs and 70 microsatellite loci. By combining information from four different neutrality tests, in total ten genomic regions showed signs of directional selection based on multiple sources of evidence. Most of the identified candidate regions were rather small ranging from zero to a few centimorgans (cM) in the female Atlantic salmon linkage map. We also evaluated how adaptation from standing variation affects adjacent SNP and microsatellite variation along the chromosomes and, by using forward simulations with strong selection, we were able to generate genetic differentiation patterns comparable to the observed data. This study highlights the significance of standing genetic variation during the early stages of adaptation and represents a useful step towards identifying functional variants involved in domestication of Atlantic salmon.